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SGAEventsInfo.py
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import MySQLdb
import csv
class SGAEventsInfo:
def __init__(self):
self.db = MySQLdb.connect("localhost", "fanyu", "hellowork", "TDI")
self.cursor = self.db.cursor()
def findGeneName(self, geneID):
query = "SELECT gene_name FROM Genes WHERE gene_id= '%s'" %(geneID)
self.cursor.execute(query)
results = self.cursor.fetchall()
return results[0][0]
def findGeneId(self, geneName):
query = "SELECT gene_id FROM Genes WHERE gene_name= '%s'" %(geneName)
self.cursor.execute(query)
results = self.cursor.fetchall()
return results[0][0]
def findPatient(self, patient_id):
query = "SELECT name FROM Patients WHERE patient_id= '%s'" %(patient_id)
self.cursor.execute(query)
results = self.cursor.fetchall()
return results[0][0]
def findDriverTumor(self, geneId):
query = "SELECT T.patient_id, T.DEG_id FROM TDI_Results as T, SGAPPNoiseThreshold as S\
WHERE T.exp_id = 1 AND T.posterior >= S.threshold AND T.SGA_id = '%s' AND T.SGA_id = S.gene_id" %(geneId)
self.cursor.execute(query)
query_results = self.cursor.fetchall()
#key : (tumorid)
#value : DEG_id
tumor_DEG = {}
for row in query_results:
if tumor_DEG.has_key(row[0]):
tumor_DEG[row[0]].append(row[1])
else :
tumor_DEG[row[0]] = []
tumor_DEG[row[0]].append(row[1])
#filter out SGA which regulate less than 5 degs
tumor_DEG = dict((k,v) for k, v in tumor_DEG.iteritems() if len(v) >= 5)
return tumor_DEG
def countSGAEvents(self, geneId):
query = "SELECT COUNT(DISTINCT patient_id) FROM SGAs WHERE gene_id = '%s'" %(geneId)
self.cursor.execute(query)
query_results = self.cursor.fetchall()
return query_results[0][0]
#filter out drivers that has been called driver less than a certain number of tumors
def findSMEvents(self, geneId, tumor_DEG):
query = "SELECT DISTINCT patient_id FROM Somatic_Mutations WHERE gene_id = '%s' AND protein_func_impact = 1" %(geneId)
self.cursor.execute(query)
query_results = self.cursor.fetchall()
numberOfSMEvents = len(query_results)
if (numberOfSMEvents != 0):
numberOfSMDriverCall = 0
for row in query_results:
if tumor_DEG.has_key(row[0]):
numberOfSMDriverCall += 1
return (numberOfSMEvents, numberOfSMDriverCall, float(numberOfSMDriverCall)/numberOfSMEvents)
else:
return (0, 0, "NaN")
def findSCNAmpvents(self, geneId, tumor_DEG):
query = "SELECT DISTINCT patient_id FROM SCNAs WHERE gene_id = '%s' AND gistic_score = 2" %(geneId)
self.cursor.execute(query)
query_results = self.cursor.fetchall()
numberOfSCNAmpEvents = len(query_results)
if (numberOfSCNAmpEvents != 0):
numberOfSCNAmpDriverCall = 0
for row in query_results:
if tumor_DEG.has_key(row[0]):
numberOfSCNAmpDriverCall += 1
return (numberOfSCNAmpEvents, numberOfSCNAmpDriverCall, float(numberOfSCNAmpDriverCall)/numberOfSCNAmpEvents)
else:
return (0, 0, "NaN")
def findSCNDelEvents(self, geneId, tumor_DEG):
query = "SELECT DISTINCT patient_id FROM SCNAs WHERE gene_id = '%s' AND gistic_score = -2" %(geneId)
self.cursor.execute(query)
query_results = self.cursor.fetchall()
numberOfSCNDelEvents = len(query_results)
if (numberOfSCNDelEvents != 0):
numberOfSCNDelDriverCall = 0
for row in query_results:
if tumor_DEG.has_key(row[0]):
numberOfSCNDelDriverCall += 1
return (numberOfSCNDelEvents, numberOfSCNDelDriverCall, float(numberOfSCNDelDriverCall)/numberOfSCNDelEvents)
else:
return (0, 0, "NaN")
def findSGAEventsInforForAllSGA(self):
# cursor = self.db.cursor()
# query = "SELECT DISTINCT gene_id FROM SGAs WHERE gene_id IS NOT NULL"
# cursor.execute(query)
# query_results = cursor.fetchall()
tableName = "SGAEvents"
drivers = self.findDriver(30)
print len(drivers)
with open("%s.csv"%(tableName), 'wb') as csvfile:
writer=csv.writer(csvfile, delimiter=',',)
writer.writerow(["SGA", "#SGAEvents", "#SGA-FI Call", "CallRate", "#SMEvents", "#SM-FI Call", "SMCallRate", "#SCNAmpEvents", "#SCNAmp-FI call", "SCNAmp-FICallRate", "#SCNDelEvents", "#SCNDel-FI call", "SCNDel-FICallRate"])
# for row in query_results:
# driver = row[0]
for driver in drivers:
numberOfSGAEvents = self.countSGAEvents(driver)
if (numberOfSGAEvents >= 30):
tumor_DEG = self.findDriverTumor(driver)
numberOfSGADriverCall = len(tumor_DEG.keys())
SGAEventsInfo = (numberOfSGAEvents, numberOfSGADriverCall, float(numberOfSGADriverCall)/numberOfSGAEvents)
SMEventsInfo = self.findSMEvents(driver, tumor_DEG)
SCNAmpEventsInfo = self.findSCNAmpvents(driver, tumor_DEG)
SCNDelEventsInfo = self.findSCNDelEvents(driver, tumor_DEG)
SGA = self.findGeneName(driver)
print SGA
# print SGAEventsInfo
# print SMEventsInfo
# print SCNAmpEventsInfo
# print SCNDelEventsInfo
writer.writerow([SGA, SGAEventsInfo[0], SGAEventsInfo[1], SGAEventsInfo[2], SMEventsInfo[0], SMEventsInfo[1], SMEventsInfo[2], SCNAmpEventsInfo[0], SCNAmpEventsInfo[1], SCNAmpEventsInfo[2], SCNDelEventsInfo[0], SCNDelEventsInfo[1], SCNDelEventsInfo[2]])
print "done"
def findDriver(self, threshold):
#find all TDI records that satisfy the posterior threshold
query = "SELECT T.patient_id, T.SGA_id, T.DEG_id FROM TDI_Results as T, SGAPPNoiseThreshold as S\
WHERE T.exp_id = 1 AND T.posterior >= S.threshold AND T.SGA_id = S.gene_id"
self.cursor.execute(query)
query_results = self.cursor.fetchall()
#organize TDI records to a dictionary, key is (tumorid , SGA_id), value is DEG_id
tumor_SGA = {}
for row in query_results:
temp_tuple = (row[0], row[1])
if tumor_SGA.has_key(temp_tuple):
tumor_SGA[temp_tuple].append(row[2])
else :
tumor_SGA[temp_tuple] = []
tumor_SGA[temp_tuple].append(row[2])
#filter out SGA which regulate less than 5 degs
tumor_SGA = dict((k,v) for k, v in tumor_SGA.iteritems() if len(v) >= 5)
#extract driver from dictionary tumor_SGA
SGA_tumor = {}
for key in tumor_SGA:
if SGA_tumor.has_key(key[1]):
SGA_tumor[key[1]].append(key[0])
else:
SGA_tumor[key[1]] = []
SGA_tumor[key[1]].append(key[0])
SGA_tumor_subset = dict((k,v) for k, v in SGA_tumor.iteritems() if len(v) >= threshold)
return SGA_tumor_subset.keys()
def main():
tdi = SGAEventsInfo()
tdi.findSGAEventsInforForAllSGA()
if __name__ == "__main__":
main()